Modification of target proteins by ubiquitin and ubiquitin-like polypeptides has emerged as a major mechanism for regulating many cellular processes ranging from metabolic control to cell cycle progression. In turn, these intracellular functions translate into key roles for ubiquitin modification systems in the control of complex regulatory programs at the organismal level including differentiation, development, circadian rhythms, and storage of memories. Although our knowledge of the biological functions of ubiquitin modification systems has exploded over the past decade, our understanding of how these systems operate at a biochemical level remains relatively modest. However, the past few years have witnessed a tremendous surge in the availability of three dimensional structures of components of these modification systems, which is beginning to foster a deeper understanding of how these proteins work. In addition, novel proteomic and functional genomic tools are revealing new functions for components of ubiquitin modification systems, and shedding light on how modification enzymes and substrates are linked together into networks. The objective of the third Cold Spring Harbor meeting on Ubiquitin is to bring together investigators who study the biochemical and structural properties of ubiquitin modification systems with investigators who focus on their biological functions and systems architecture. Given the rapid developments over the past two years, this meeting presents a exciting opportunity for participants to learn about recent developments that will be relevant to their own research. The program will include 8 sessions covering the components of ubiquitin modification systems and the cellular and organismal processes that they control. The sessions will be led by two outstanding and well-known investigators in these areas. With the exception of overview talks presented by the session chairs, all of the talks and posters to be presented will be selected from submitted abstracts, and most of the talks will be given by students, postdoctoral fellows and other younger investigators. It is expected that more than 275 scientists will attend. Of these, over half are likely to be graduate students and postdoctoral fellows. The subsequent meetings (2009 and 2011) will follow a similar format which will include topics that are highly relevant to the current research at the time of the meeting.